US7003175B2 - Object-order multi-planar reformatting - Google Patents
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- MPR multi-planar reformatting
- MR magnetic resonance
- CT computed tomography
- PET positron emission tomography
- seismic data measurements are also stored in very large three-dimensional volumes with as many as 2048 ⁇ 2048 ⁇ 2048 grid elements for a total of over 8.5 billion data values.
- RAM random-access memory
- Some three-dimensional arrays can be so large that their size exceeds the memory addressing capability of 32-bit central processing units (“CPU”s) found in many personal computers and graphics workstations, which CPUs may be limited to addressing a maximum of 4.2 billion data elements.
- MPR has heretofor been implemented as an image-order technique, where the pixel locations of the cross-sectional image are generated and traversed sequentially, transformed in the coordinate system of the volume data, and interpolated over a data neighborhood of the three-dimensional array.
- one limitation of current MPR methods is that they require random access to the data values of the three-dimensional array, and therefore the entire array needs to be stored in the computer's RAM.
- a costly apparatus with very large amounts of RAM is typically needed.
- Another limitation of current methods is that when using a 32-bit CPU, for example, the size of the three-dimensional array used for MPR is limited to the maximum number of data elements addressable by the CPU. Thus, a need exists to remove these limitations in order to permit an apparatus and/or programmed computer having a limited amount of memory to compute MPR cross-sectional images of very large three-dimensional arrays, which arrays may be composed of an arbitrarily large number of slices.
- a system and method for object-order reformatting of a volume having data slices that includes a coordinate transformation unit for transforming coordinates of an oblique surface through the volume from image-order to object-order, an object-order slice traversal unit for traversing the slices in accordance with the object-order of the transformed coordinates, and a slice-pair interpolation unit for interpolating voxel values of a pair of adjacent slices to render pixel values for an image of the oblique plane.
- FIG. 1 shows a block diagram of a system for object-order reformatting of large volumes according to an illustrative embodiment of the present disclosure
- FIG. 2 a shows a schematic slice comprising a two-dimensional grid of picture elements (“pixels”);
- FIG. 2 b shows a schematic series of slices of FIG. 2 a arranged in sequential order
- FIG. 2 c shows a schematic volume formed from the series of slices of FIG. 2 b comprising a three-dimensional grid of volume elements (“voxels”);
- FIG. 2 d shows a schematic neighborhood of 8 adjacent voxels
- FIG. 3 a shows a schematic multi-planar reformatting (“MPR”) image and its two-dimensional pixel coordinates
- FIG. 3 b shows a schematic transformed MPR plane of FIG. 3 a and its three-dimensional pixel coordinates
- FIG. 3 c shows the schematic MPR plane of FIG. 3 b positioned through a volume in order to compute the MPR image of an oblique cross-section
- FIG. 4 shows a schematic three-dimensional volume as seen from its x-axis, the position of the series of slices in such volume, an oblique cross-section through such volume, and the position of samples along scan lines of such oblique cross-section;
- FIG. 5 shows a block flow diagram of the object-order MPR method
- FIG. 6 a shows an exemplary list of unsorted elements
- FIG. 6 b shows an exemplary list of sorted linked-list elements.
- a system and method are disclosed for computing an image of an oblique cross-section from a three-dimensional volume object composed of a series of parallel slices, where the order of processing is based on the progressive traversal of slices in the three-dimensional volume object (i.e., “object-order”) rather than being based on the progressive traversal of pixels in the computed multi-planar reformatted image (i.e., “image-order”).
- the series of parallel slices contains data values representing the interior of a three-dimensional volume, such as, for example, data from magnetic resonance (“MR”) scanners.
- MR magnetic resonance
- the orientation of the oblique cross-section is specified as a transform composed of rotation, translation, shear, and scaling with respect to a chosen coordinate system.
- the transformed coordinates of the pixels in the cross-sectional image are computed incrementally and sorted according to the progressive slice order of the volume.
- the sorted coordinates are then traversed and pixel values of the MPR image are interpolated from the corresponding neighborhood of data values in data space.
- FIG. 1 shows a block diagram of a system 100 for object-order reformatting of large volumes according to an illustrative embodiment of the present disclosure.
- the system 100 includes at least one processor or central processing unit (“CPU”) 102 in signal communication with a system bus 104 .
- CPU central processing unit
- a read only memory (“ROM”) 106 , a random access memory (“RAM”) 108 , a display adapter 110 , an I/O adapter 112 , and a user interface adapter 114 are also in signal communication with the system bus 104 .
- a display unit 116 is in signal communication with the system bus 104 via the display adapter 110 .
- a disk storage unit 118 such as, for example, a magnetic or optical disk storage unit, is in signal communication with the system bus 104 via the I/O adapter 112 .
- a mouse 120 , a keyboard 122 , and an eye tracking device 124 are also in signal communication with the system bus 104 via the user interface adapter 114 . The mouse 120 , keyboard 122 , and eye-tracking device 124 are used to aid in the generation of selected regions in an image.
- a coordinate transformation unit 170 , an object-order slice traversal unit 180 and a slice-pair interpolation unit 190 are also included in the system 100 and in signal communication with the CPU 102 and the system bus 104 . While the coordinate transformation unit 170 , the object-order slice traversal unit 180 and the slice-pair interpolation unit 190 are illustrated as coupled to the at least one processor or CPU 102 , these components are preferably embodied in computer program code stored in at least one of the memories 106 , 108 and 118 , wherein the computer program code is executed by the CPU 102 .
- the system 100 may also include a digitizer 126 in signal communication with the system bus 104 via a user interface adapter 114 for digitizing an image slice.
- the digitizer 126 may be omitted, in which case digital image slices may be input to the system 100 from a network via a communications adapter 128 in signal communication with the system bus 104 , or via other suitable means as understood by those skilled in the art.
- FIGS. 2 a through 2 d a slice composed of a two-dimensional grid of picture elements (“pixels”) is indicated generally by the reference numeral 210 , and an (x,y) pixel 211 is shown in FIG. 2 a .
- a Z-axis sequence of image slices 210 is illustrated in FIG. 2 b .
- a 3-dimensional volume 213 comprising the image slices 210 and a voxel neighborhood 212 is shown in FIG. 2 c , along with a representative voxel value 214 .
- the voxel neighborhood 212 and eight adjacent voxel values 214 through 228 are shown in FIG. 2 d.
- FIG. 3 a illustrates an MPR image 310 having a two-dimensional (x,y) pixel coordinate 312 .
- FIG. 3 b illustrates a transformed MPR plane 314 having a three-dimensional (x,y,z) pixel coordinate 316 .
- FIG. 3 c illustrates an MPR plane oblique cross-section 318 positioned through a volume 313 in order to compute the MPR image of the oblique cross-section 318 .
- FIG. 4 illustrates a three-dimensional volume 413 as seen from its X-axis, the positions of the series of slices 421 through 426 in the volume, an oblique cross-section 418 through the volume, and the positions of samples 430 along each scan line 432 of the oblique cross-section 418 .
- seven samples 430 are shown along each of seven scan lines 432 .
- FIG. 5 a block flow diagram of the object-order MPR method is indicated generally by the reference numeral 510 .
- Function block 512 performs oblique plane orientation and passes control to function block 514 .
- Block 514 performs image-order coordinate transformation and passes control to function block 516 .
- Block 516 performs object-order sorting, and passes to function block 518 if any (x,y) coordinates remain, or to function block 520 if all coordinates have been sorted.
- Block 518 passes control back to block 514 for each (x,y) coordinate.
- Block 520 performs object-order slice traversal and passes control to function block 522 , which computes object-order voxel coordinates and passes control to function block 524 .
- Block 524 performs slice-pair interpolation, and passes control to function block 526 if any coordinates remain for the current slice, or to function block 528 to process the next slice.
- Block 526 passes control back to block 522 for each coordinate of the current slice.
- Block 528 passes control back to block 520 to perform object-order slice traversal for each remaining slice, or to function block 530 if all slices have been traversed.
- Function block 530 outputs the MPR image as determined by the object-order technique.
- FIGS. 6 a and 6 b illustrate the data structures used in a preferred embodiment.
- FIG. 6 a shows an exemplary unsorted list 610 of unsorted elements 612 and a corresponding pointer array 614 .
- FIG. 6 b shows an exemplary sorted linked-list 616 of sorted elements 618 and a corresponding pointer array 620 .
- data acquisition includes assembling a three-dimensional volume array of data from a regular succession of adjacent “slices” through the object being scanned, where each slice is a two-dimensional image array of data points.
- the derivation of such three-dimensional volume array is well known in the art and readily obtainable using systems such as magnetic resonance (“MR”) imaging systems, computed tomography (“CT”) scanning systems, positron emission tomography (“PET”), and ultrasound scanning.
- MR magnetic resonance
- CT computed tomography
- PET positron emission tomography
- ultrasound scanning Each grid value of a two-dimensional image array is called a picture element, or “pixel”.
- Each grid value of a three-dimensional volume array is called a volume element, or “voxel”.
- M fwd T ( Dx,Dy,Dz ) ⁇ R ( ⁇ , ⁇ , ⁇ ) ⁇ S ( Sx,Sy,Sz ) ⁇ G ( ⁇ , ⁇ ) (2)
- T is a translation matrix
- R is a rotation matrix
- S is a scaling matrix
- G is a gantry tilt (“shear”) matrix in the following form:
- T ⁇ ( D ⁇ ⁇ x , D ⁇ ⁇ y , D ⁇ ⁇ z ) [ 1 0 0 0 1 0 0 0 0 1 0 D ⁇ ⁇ x D ⁇ ⁇ y D ⁇ ⁇ z 1 ] ( 3 )
- (Dx, Dy, Dz) are translation coefficients
- (Sx, Sy, Sz) are scaling coefficients
- ( ⁇ , ⁇ , ⁇ ) are rotation angles
- ( ⁇ , ⁇ ) are gantry angles.
- the matrix G is used in order to compensate for the x and y gantry tilt angle adjustment of certain medical scanners.
- Matrix M fwd represents a forward mapping of the three-dimensional volume array onto the coordinate system of a projection plane.
- the inverse matrix form can be used: M i ⁇ ⁇ x ⁇ ⁇ u i ⁇ ⁇ x ⁇ ⁇ v i ⁇ ⁇ x ⁇ ⁇ w 0 i ⁇ ⁇ y ⁇ ⁇ u i ⁇ ⁇ y ⁇ ⁇ v i ⁇ ⁇ y ⁇ w 0 i ⁇ z ⁇ u i ⁇ ⁇ z ⁇ v i ⁇ z ⁇ w 0 i ⁇ ⁇ t ⁇ u i ⁇ ⁇ t ⁇ u i ⁇ ⁇ t ⁇ ⁇
- M inv is the inverse of matrix M fwd , and can be used as the transformation matrix for the MPR image plane of an oblique cross-section at any arbitrary angle, scale and position as specified by the user.
- the computation of [x′,y′,z′] coordinates is performed incrementally. More specifically, the matrix coefficients of equation (7) are used directly in order to compute [x′,y′,z′] coordinates instead of transforming each [x,y] coordinate with a matrix multiplication as in equation (8).
- the translation coefficients itu, itv, itw can be used as the coordinates of the origin of the oblique plane.
- the start point of each scan line can be computed by adding the coefficients iyu, iyv, iyw incrementally to the origin of the oblique plane.
- Each successive point along a scan line can be computed by adding the coefficients ixu, ixv, ixw incrementally to the start point of each scan line.
- FIG. 2 illustrates how the [x,y] coordinates on an MPR image are transformed into [x′,y′,z′] coordinates of an MPR plane, which is positioned through a volume in order to compute the MPR image of an oblique cross-section.
- the object-order MPR method disclosed herein is not limited to planar oblique planes, but can also be used with curved oblique planes, where a series of [x,y] coordinates defining a two-dimensional curve can be transformed using equation (8), and then extruded along a third axis incrementally using the izu, izv, izw coefficients of equation (8).
- Equation (8) computes the transformed [x′,y′,z′] coordinates from [x,y] coordinates of the image plane, and shows MPR to be image-order dependent.
- This image-order dependency causes very inefficient arbitrary memory access to slices in the three-dimensional volume array.
- the oblique plane crosses the volume with an orientation orthogonal to the slices, each slice is visited numerous times while traversing the coordinates of each image scan line.
- FIG. 4 where a low-resolution 2D representation of the volume and of the oblique plane is used for sake of simplicity. Note how the seven samples of the first or upper scan line traverse the slices 423 , 424 , 425 , 426 of the volume, and then the samples of the adjacent scan line traverse slices 423 , 424 , 425 , 426 once again.
- Embodiments of the present disclosure remove the limitation of such image-order dependency by processing the [x,y] pixels of the image plane based on the progressive order of the volume slices, thereby implementing an object-order method.
- a computer apparatus could load volume slices in memory sequentially, and perform tri-linear interpolation using only two adjacent slices in memory (slice iz and slice iz+1). Slices could be loaded into memory sequentially, and after all the samples associated with a slice pair have been interpolated, the slices could be progressively unloaded from memory.
- a low-cost computer using an object-order MPR algorithm could compute cross-sections of volumes with an arbitrary number of slices (even several thousands of them), because all it is needed is enough memory to store two slices at any time.
- the present disclosure introduces a Sorting Device between the [x′,y′,z′] coordinate generation step and the tri-linear interpolation step.
- the minimum requirement for such a Sorting Device is to rearrange and sort [x′,y′,z′] coordinates according to the progressive ordering of slices in the three-dimensional array.
- the scan lines of each slice as well as the pixels in each scan line are also sorted in progressive order.
- the interpolation of the MPR image can be executed in object-order rather than in image-order.
- FIG. 4 depicts a block diagram of the herein described object-order MPR method.
- the sorting device may comprise special purpose high-speed integrated circuit chips to perform the reordering of the coordinates; or it may be implemented by a programmed computer, with either a serial processor or parallel processors.
- the sorting device is implemented by a programmed computer, which reorders the [x′y′z′] coordinates progressively using linked-list structures. More specifically, a list called NodeList is allocated, containing as many elements as the total number of pixels in the MPR image. Each element of such list is called a “Node”, and stores the following information: an [x,y] offset into the MPR image plane, the corresponding transformed [x′,y′,z′] coordinate value, and a nodeLink variable containing a link to another Node in the list.
- the sorting step consists in storing each computed [x,y] and [x′,y′,z′] values in a Node, and then link together Node elements which have the same integer part value of z′ (i.e. Nodes having the same value of iz).
- a list called BinList is allocated, containing as many elements as the total number of slices.
- Each element of such list is called a “Bin”, and stores the following information for each slice: a firstNode link to the first Node having the corresponding iz slice index, and a lastNode link to the last Node added to the linked list of Nodes for the corresponding iz slice index.
- BinList will hold a series of variable length linked-lists of Nodes for each slice. This reordering process is illustrated in FIGS. 5 a and 5 b , where a series of disjointed Nodes depicted in FIG. 5 a is progressively linked in slice order, as depicted in FIG. 5 b .
- One exemplary implementation embodiment is shown in the following pseudo-code listing:
- This pseudo-code implements the image-order computation of [x′,y′,z′] coordinates of an oblique planar cross-section and the progressive object-order sorting using linked-list structures. As an additional optimization, if any of the transformed coordinates fall outside the range of the three-dimensional volume array, they are discarded and do not get stored in the sorted linked-list structure.
- the sorting device After the sorting device has sorted the coordinates in object-order, the sorted coordinates are traversed in a slice-by-slice fashion, and tri-linear interpolation is performed using values from the current slice and its neighboring slice.
- int(n) represents the integer part of n (i.e. the part before the decimal point)
- frac(n) represents the fractional part of n (i.e. the part after the decimal point).
- integer [ix,iy,iz] values are used as offsets into the three-dimensional volume array. This imposes the limitation of having random access to any data value in the three-dimensional array, which in programmed computers limits the size of the array to the maximum number of addressable memory locations.
- the present disclosure removes such limitation by loading slices in memory only when they are needed, discarding them when the computer memory becomes saturated.
- V 1 pixel[ ix,iy] of slice iz
- V 2 pixel[ ix+ 1 ,iy] of slice iz
- V 3 pixel[ ix,iy+ 1] of slice iz
- V 4 pixel[ ix+ 1 ,iy+ 1] of slice iz
- V 5 pixel[ ix,iy] of slice iz+ 1 (11)
- V 6 pixel[ ix+ 1 ,iy] of slice iz+ 1
- V 7 pixel[ ix,iy+ 1] of slice iz+ 1
- V 8 pixel[ ix+ 1 ,iy+ 1] of slice iz+ 1
- the MPR image pixels are first initialized to zero.
- Each element of BinList is examined sequentially, and if the value of firstNode is not zero, the corresponding Node structure is retrieved.
- the information stored in the Node structure is used to determine which two slices are needed in memory, and tri-linear interpolation is performed using equations (10) through (12).
- the nodeLink variable of Node is examined, and if it is not zero, the corresponding linked Node is retrieved and the interpolation step is repeated until all linked Nodes of a particular Bin have been used.
- One implementation of the object-order traversal of the linked-list structures is shown in the following pseudo-code listing:
- This linked-list traversal for a specific Bin guarantees that all the samples requiring a specific pair of slices for tri-linear interpolation will be computed before moving to a new pair of slices.
- the interpolation process continues until every linked-list of Nodes of every Bin has been traversed and processed in object-order.
- Embodiments of the present disclosure provide a method of the type initially described wherein an image of an oblique cross-section (i.e., an MPR image) can be efficiently computed, even when the entire three-dimensional array containing the data being interpolated is extremely large and exceeds the memory storage and memory addressing capabilities of the processing apparatus.
- an image of an oblique cross-section i.e., an MPR image
- the set of transformed image-order coordinates necessary for the computation of an oblique cross-section are rearranged by a sorting device, which generates a list of coordinates sorted according to the progressive order of the slices in the three-dimensional data.
- the sorted coordinates are then traversed in object-order, allowing the processing apparatus to require only a minimum amount of memory for the storage and addressing of two slices, thereby reducing the overall cost of the processing apparatus and allowing such processing apparatus to compute oblique cross-sections of very large three-dimensional arrays containing thousands of slices.
- an advantage of object-order processing is that the parallel slices of the object are traversed progressively, one at a time, and interpolated using slice pairs. Therefore, the storage memory requirements of any apparatus used for computing the oblique cross-section can be greatly reduced, because only two slices need to reside in memory at any time, and each slice is loaded in memory only once.
- the low memory requirements of the disclosed object-order method permit a simple processing apparatus or programmed computer with limited memory to compute oblique cross-sections of very large three-dimensional volumes containing an arbitrarily large number of slices.
- the teachings of the present disclosure are implemented as a combination of hardware and software.
- the software is preferably implemented as an application program tangibly embodied on a program storage unit.
- the application program may be uploaded to, and executed by, a machine comprising any suitable architecture.
- the machine is implemented on a computer platform having hardware such as one or more central processing units (“CPU”), a random access memory (“RAM”), and input/output (“I/O”) interfaces.
- CPU central processing units
- RAM random access memory
- I/O input/output
- the computer platform may also include an operating system and microinstruction code.
- the various processes and functions described herein may be either part of the microinstruction code or part of the application program, or any combination thereof, which may be executed by a CPU.
- various other peripheral units may be connected to the computer platform such as an additional data storage unit and a printing unit.
Abstract
Description
M fwd =T(Dx,Dy,Dz)·R(α,β,γ)·S(Sx,Sy,Sz)·G(Φ,θ) (2)
iz=int(z′) (9)
allocate NodeList[number of pixels in MPR image] |
allocate BinList[number of slices in volume] |
set all listOfBins elements to zero |
line.setPosition(itu, itv, itw) |
nodeIndex = 0 |
for y = 0 to image.height-1 |
point.setPosition(line.x, line.y, line.z) | |
for x = 0 to image.width-1 |
if(point is inside valid array boundaries) |
NodeList[nodeIndex].setCoordinate3D(point) | |
NodeList[nodeIndex].setCoordinate2D(x,y) | |
NodeList[nodeIndex].nodeLink = 0 | |
iz = int(point.z) | |
if(BinList[iz] is empty) |
BinList[iz].firstNode = link to (NodeList[nodeIndex]) | |
BinList[iz].lastNode = link to (NodeList[nodeIndex]) |
else |
previousNode = BinList[iz].lastNode | |
previousNode.nodeLink = link to (NodeList[nodeIndex]) | |
BinList[iz].LastNode = link to (NodeList[nodeIndex]) |
endIf | |
nodeIndex = nodeIndex + 1 |
endIf | |
point.setPosition(point.x + ixu, point.y + ixv, point.z + ixw) |
next x | |
line.setPosition(line.x + iyu, line.y + iyv, line.z + iyw) |
next y |
[ix iy iz]=[int(x′)int(y′)int(z′)]
[fx fy fz]=[frac(x′)frac(y′)frac(z′)] (10)
V 1=pixel[ix,iy] of slice iz
V 2=pixel[ix+1,iy] of slice iz
V 3=pixel[ix,iy+1] of slice iz
V 4=pixel[ix+1,iy+1] of slice iz
V 5=pixel[ix,iy] of slice iz+1 (11)
V 6=pixel[ix+1,iy] of slice iz+1
V 7=pixel[ix,iy+1] of slice iz+1
V 8=pixel[ix+1,iy+1] of slice iz+1
A=V 1 +fx*(V 2 −V 1)
B=V 3 +fx*(V 4 −V 3)
C=V 5 +fx*(V 6 −V 5)
D=V 7 +fx*(V 8 −V 7)
E=A+fy*(B−A) (12)
F=C+fy*(D−C)
V=E+fz*(F−E)
pixel[x,y] of MPR image=V
initialize all MPR pixel values to zero | ||
for every slice z in the volume |
currentNode = BinList[z].firstNode | |
while currentNode is not zero |
MPRimage.pixelValue(currentNode.coordinate2D) = |
interpolate(currentNode.coordinate3D) |
currentNode = currentNode.nodeLink |
end while |
next z | ||
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